Journal of Microbiology

Journal Article

Intestinal Lactobacillus community structure and its correlation with diet of Southern Chinese elderly subjects§: Yuanyuan Pan , Da-Wen Sun , Quanyang Li; J. Microbiol. 2016;54(9):594-601. Published online August 31, 2016; DOI: https://doi.org/10.1007/s12275-016-6131-7

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This study aimed to investigate the relationship between the intestinal Lactobacillus species and diet of elderly subjects in a longevity area in Southern China. Healthy elderly subjects ranging from 80 to 99 years old were respectively selected from the regions of Bama and Nanning, Guangxi, China. The nested polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) technology was used to analyze the intestinal Lactobacillus community structure.
Results
showed that Weissella confusa, L. mucosae, L. crispatus, L. salivarius, and L. delbrueckii were the representative Lactobacillus of elderly subjects. Among them, L. crispatus and L. delbrueckii were the dominant Lactobacillus of all species. In comparison to Nanning elderly subjects, the detection frequencies of W. confusa and L. salivarius were significantly increased in Bama elderly subjects (P < 0.01), whereas L. mucosae was significantly decreased (P < 0.01). Interestingly, it was also found that there were 4 kinds of representative Lactobacillus, which were significantly correlated with dietary fiber. W. confusa (P < 0.01) and L. salivarius (P < 0.05) were significantly positively correlated with the intake of dietary fiber, while L. mucosae (P < 0.01) and L. crispatus (P < 0.05) were significantly negatively correlated with the intake of dietary fiber, respectively. Results confirmed that different diets had obvious effects on the intestinal Lactobacillus community structure of elderly subjects in Southern China, which may provide a certain theoretical basis for the elderly’s healthy food strategic design and probiotics product development.

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Research Support, Non-U.S. Gov't

Effect of Fumarate Reducing Bacteria on In Vitro Rumen Fermentation, Methane Mitigation and Microbial Diversity: Lovelia Mamuad , Seon Ho Kim , Chang Dae Jeong , Yeon Jae Choi , Che Ok Jeon , Sang-Suk Lee; J. Microbiol. 2014;52(2):120-128. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3518-1

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Abstract

The metabolic pathways involved in hydrogen (H2) production, utilization and the activity of methanogens are the important factors that should be considered in controlling methane (CH4) emissions by ruminants. H2 as one of the major substrate for CH4 production is therefore should be controlled. One of the strategies on reducing CH4 is through the use of hydrogenotrophic microorganisms such as fumarate reducing bacteria. This study determined the effect of fumarate reducing bacteria, Mitsuokella jalaludinii, supplementation on in vitro rumen fermentation, CH4 production, diversity and quantity. M. jalaludinii significantly reduced CH4 at 48 and 72 h of incubation and significantly increased succinate at 24 h. Although not significantly different, propionate was found to be highest in treatment containing M. jalaludinii at 12 and 48 h of incubation. These results suggest that supplementation of fumarate reducing bacteria to ruminal fermentation reduces CH4 production and quantity, increases succinate and changes the rumen microbial diversity.

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Journal Article

Detecting Nonculturable Bacteria in the Active Mycorrhizal Zone of the Pine Mushroom Tricholoma matsutake: Ryota Kataoka , Zaki Anwar Siddiqui , Junichi Kikuchi , Masaki Ando , Rina Sriwati , Ai Nozaki , Kazuyoshi Futai; J. Microbiol. 2012;50(2):199-206. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1371-7

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Abstract: The fungus Tricholoma matsutake forms an ectomycorrhizal relationship with pine trees. Its sporocarps often develop in a circle, which is commonly known as a fairy ring. The fungus produces a solid, compact, white aggregate of mycelia and mycorrhizae beneath the fairy ring, which in Japanese is called a ‘shiro’. In the present study, we used soil dilution plating and molecular techniques to analyze the bacterial communities within, beneath, and outside the T. matsutake fairy ring. Soil dilution plating confirmed previous reports that bacteria and actinomycetes are seldom present in the soil of the active mycorrhizal zone of the T. matsutake shiro. In addition, the results showed that the absence of bacteria was strongly correlated with the presence of T. matsutake mycorrhizae. The results demonstrate that bacteria, especially aerobic and heterotrophic forms, and actinomycetes, are strongly inhibited by T. matsutake. Indeed, neither bacteria nor actinomycetes were detected in 11.3% of 213 soil samples from the entire shiro area by culture-dependent
methods
. However, molecular techniques demonstrated that some bacteria, such as individual genera of Sphingomonas and Acidobacterium, were present in the active mycorrhizal zone, even though they were not detected in soil assays using the dilution plating technique.

Research Support, Non-U.S. Gov'ts

Lactobacillus salivarius REN Counteracted Unfavorable 4-Nitroquinoline-1-Oxide-Induced Changes in Colonic Microflora of Rats: Ming Zhang , Xuewei Qiao , Liang Zhao , Lu Jiang , Fazheng Ren; J. Microbiol. 2011;49(6):877-883. Published online December 28, 2011; DOI: https://doi.org/10.1007/s12275-011-1137-7

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14 Scopus

Abstract: Probiotics and carcinogens both have a significant effect on the microfloral composition of the human intestine. The objective of this study was to investigate the impact of an important carcinogen, 4-Nitroquinoline-1- Oxide on colonic microflora and the efficacy of the probiotic Lactobacillus salivarius REN as an agent of counteracting these effects. Using denaturing gradient gel electrophoresis (DGGE) combined with redundancy analysis, we demonstrated that both 4-Nitroquinoline-1-Oxide and L. salivarius REN significantly altered the bacterial communities of rat colons. A total of 27 bacterial strains were identified as being affected by treatment with 4-Nitroquinoline-1-Oxide or L. salivarius REN using a t-value biplot combined with band sequencing. 4-Nitroquinoline-1-Oxide treatment increased the abundance of two potential pathogens (one Helicobacter strain and one Desulfovibrio strain), as well as reducing the abundance of two potentially beneficial strains (one Ruminococcaceae strain and one Rumen bacteria). The Helicobacter strain was initally detected in carcinogen-treated rat intestinal microflora, but L. salivarius REN treatment effectively suppressed the growth of the Helicobacter strain. These results suggested that L. salivarius REN may be a potential probiotic, efficiently acting against the initial infection with, and the growth of pathogenic bacteria.

Comparative Approach to Capture Bacterial Diversity of Coastal Waters: Hyunsoo Na , Ok-Sun Kim , Seok-Hwan Yoon , Yunmin Kim , Jongsik Chun; J. Microbiol. 2011;49(5):729-740. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1205-z

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Abstract: Despite the revolutionary advancements in DNA sequencing technology and cultivation techniques, few studies have been done to directly compare these methods. In this study, a 16S rRNA gene-based, integrative approach combining culture-independent techniques with culture-dependent methods was taken to investigate the bacterial community structure of coastal seawater collected from the Yellow Sea, Korea. For culture-independent studies, we used the latest model pyrosequencer, Roche/454 Genome Sequencer FLX Titanium. Pyrosequencing captured a total of 52 phyla including 27 candidate divisions from the water column, whereas the traditional cloning approach captured only 15 phyla including 2 candidate divisions. In addition, of 878 genera retrieved, 92.1% of the sequences were unique to pyrosequencing. For culture-dependent analysis, plate culturing, plate washing, enrichment, and high-throughput culturing (HTC) methods were applied. Phylogenetic analysis showed that the plate-washing clones formed a cluster devoid of any previously cultured representatives within the family Rhodobacteraceae. One HTC isolate (SF293) fell into the OM182 clade, which was not recovered by other culturing methods described here. By directly comparing the sequences obtained from cultures with those from culture-independent work, we found that only 33% of the culture sequences were identical to those from clone libraries and pyrosequences. This study presents a detailed comparison of common molecular and cultivation techniques available in microbial ecology. As different methods yielded different coverage, we suggest choosing the approach after carefully examining the scientific questions being asked.

Correlations of Fecal Bacterial Communities with Age and Living Region for the Elderly Living in Bama, Guangxi, China: Liang Zhao , Xuewei Qiao , Jun Zhu , Xiaoying Zhang , Jingli Jiang , Yanling Hao , Fazheng Ren; J. Microbiol. 2011;49(2):186-192. Published online May 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0405-x

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Abstract: Bama County (Guangxi, China) is famous for its longevous population. In this study, intestinal microflora of 17 healthy elderly subjects of different ages and from different regions (rural and urban) in Bama, were analyzed by denaturing gradient gel electrophoresis (DGGE). Significant effects of age and living region on the whole intestinal bacterial communities were observed by redundancy analysis (RDA). A total of 11 bacterial strains that were correlated with age and living region were identified using a t-value biplot combined with band sequencing. Four bacterial strains were correlated with both age and living region of the elderly in Bama. Two Bacteroides strains and one Ruminococcaceae strain were abundant in the rural, younger elderly; conversely, one Desulfovibrio strain was high in the urban, older elderly. Another Bacteroidetes strain was only correlated with the participant’s age, and its abundance increased with the age of the elderly. The richness of one Clostridium sordellii strain, which was only correlated with the elderly living region, was high in the urban elderly. The study also found five other novel bacterial strains that were correlated with the age or living region of the elderly in Bama. These results expand our understanding of age- and region-effects on the intestinal microflora of the elderly and raise the possibility of developing probiotics originating from centenarians.

Effects of Crude Oil on Marine Microbial Communities in Short Term Outdoor Microcosms: Seung Won Jung , Joon Sang Park , Oh Youn Kown , Jung-Hoon Kang , Won Joon Shim , Young-Ok Kim; J. Microbiol. 2010;48(5):594-600. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0199-2

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43 Scopus

Abstract: To assess the effects of crude oil spills on marine microbial communities, 10 L outdoor microcosms were manipulated over an exposure period of 8 days. The responses of microbial organisms exposed to five crude oil concentrations in 10 to 10,000 ppm (v/v) were monitored in the microcosms. The abundance of microalgae and copepods decreased rapidly upon the addition of crude oil at concentrations over 1,000 ppm, whereas the total density of heterotrophic bacteria increased dramatically at the higher concentrations. Bacterial diversity, determined by denaturing gradient gel electrophoresis, was increased at higher concentrations. In particular, the intensity of the bands representing Jannaschia sp. and Sulfitobacter brevis increased with the addition of oil. These results indicate that crude oil spills with concentrations over 1,000 ppm seriously affected the structure of the microbial communities.

Bacterial, Archaeal, and Eukaryal Diversity in the Intestines of Korean People: Young-Do Nam , Ho-Won Chang , Kyoung-Ho Kim , Seong Woon Roh , Min-Soo Kim , Mi-Ja Jung , Si-Woo Lee , Jong-Yeol Kim , Jung-Hoon Yoon , Jin-Woo Bae; J. Microbiol. 2008;46(5):491-501. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0199-7

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Abstract

The bacterial, archaeal, and eukaryal diversity in fecal samples from ten Koreans were analyzed and compared by using the PCR-fingerprinting method, denaturing gradient gel electrophoresis (DGGE). The bacteria all belonged to the Firmicutes and Bacteroidetes phyla, which were known to be the dominant bacterial species in the human intestine. Most of the archaeal sequences belonged to the methane-producing archaea but several halophilic archarea-related sequences were also detected unexpectedly. While a small number of eukaryal sequences were also detected upon DGGE analysis, these sequences were related to fungi and stramenopiles (Blastocystis hominis). With regard to the bacterial and archaeal DGGE analysis, all ten samples had one and two prominent bands, respectively, but many individual-specific bands were also observed. However, only five of the ten samples had small eukaryal DGGE bands and none of these bands was observed in all five samples. Unweighted pair group method and arithmetic averages clustering algorithm (UPGMA) clustering analysis revealed that the archaeal and bacterial communities in the ten samples had relatively higher relatedness (the average Dice coefficient values were 68.9 and 59.2% for archaea and bacteria, respectively) but the eukaryal community showed low relatedness (39.6%).

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Nature.2016; 534(7606): 191. CrossRef
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Jean-Christophe Lagier, Sophie Edouard, Isabelle Pagnier, Oleg Mediannikov, Michel Drancourt, Didier Raoult
Clinical Microbiology Reviews.2015; 28(1): 208. CrossRef
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N. Gouba, M. Drancourt
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Corinna Bang, Ruth A. Schmitz, Franz Narberhaus
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Asja Korajkic, Laura Wegener Parfrey, Brian R. McMinn, Yoshiki Vazquez Baeza, Will VanTeuren, Rob Knight, Orin C. Shanks
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Timothy Heisel, Heather Podgorski, Christopher M. Staley, Dan Knights, Michael J. Sadowsky, Cheryl A. Gale, Megan D. Lenardon
PLOS ONE.2015; 10(2): e0116705. CrossRef
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Prem Prashant Chaudhary, Nadia Gaci, Guillaume Borrel, Paul W. O’Toole, Jean-François Brugère
Applied Microbiology and Biotechnology.2015; 99(14): 5801. CrossRef
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Nina Gouba, Didier Raoult, Michel Drancourt, Kirsten Nielsen
PLoS ONE.2014; 9(9): e106994. CrossRef
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Rosine E. Tiodjio, Akihiro Sakatoku, Akihiro Nakamura, Daisuke Tanaka, Wilson Y. Fantong, Kamtchueng B. Tchakam, Gregory Tanyileke, Takeshi Ohba, Victor J. Hell, Minoru Kusakabe, Shogo Nakamura, Akira Ueda
Scientific Reports.2014;[Epub] CrossRef
Pathogenic Eukaryotes in Gut Microbiota of Western Lowland Gorillas as Revealed by Molecular Survey
Ibrahim Hamad, Mamadou B. Keita, Martine Peeters, Eric Delaporte, Didier Raoult, Fadi Bittar
Scientific Reports.2014;[Epub] CrossRef
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Pauline D. Scanlan, Christen R. Stensvold, Mirjana Rajilić-Stojanović, Hans G.H.J. Heilig, Willem M. De Vos, Paul W. O'Toole, Paul D. Cotter
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FEMS Microbiology Reviews.2014; 38(5): 996. CrossRef
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Konstantinos Triantafyllou, Christopher Chang, Mark Pimentel
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Nadia Gaci, Guillaume Borrel, William Tottey, Paul William O’Toole, Jean-François Brugère
World Journal of Gastroenterology.2014; 20(43): 16062. CrossRef
Age, Dietary Fiber, Breath Methane, and Fecal Short Chain Fatty Acids Are Interrelated in Archaea-Positive Humans1–3
Judlyn Fernandes, Angela Wang, Wen Su, Sari Rahat Rozenbloom, Amel Taibi, Elena M. Comelli, Thomas M.S. Wolever
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Andrew Y. Koh
Current Fungal Infection Reports.2013; 7(2): 144. CrossRef
Plant and Fungal Diversity in Gut Microbiota as Revealed by Molecular and Culture Investigations
Nina Gouba, Didier Raoult, Michel Drancourt, Yolanda Sanz
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Shamayim T. Ramírez-Puebla, Luis E. Servín-Garcidueñas, Berenice Jiménez-Marín, Luis M. Bolaños, Mónica Rosenblueth, Julio Martínez, Marco Antonio Rogel, Ernesto Ormeño-Orrillo, Esperanza Martínez-Romero
Applied and Environmental Microbiology.2013; 79(1): 2. CrossRef
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Young-Do Nam, Sung-Hun Yi, Seong-Il Lim
Food Control.2012; 28(1): 135. CrossRef
The domain Archaea in human mucosal surfaces
F. Matarazzo, A.C. Ribeiro, M. Faveri, C. Taddei, M.B. Martinez, M.P.A. Mayer
Clinical Microbiology and Infection.2012; 18(9): 834. CrossRef
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PLoS ONE.2012; 7(7): e40888. CrossRef
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Microbial Ecology.2011; 61(2): 353. CrossRef
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Andrew P. A. Oxley, Mariana P. Lanfranconi, Dieco Würdemann, Stephan Ott, Stefan Schreiber, Terry J. McGenity, Kenneth N. Timmis, Balbina Nogales
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Characterization of the Depth-Related Changes in the Microbial Communities in Lake Hovsgol Sediment by 16S rRNA Gene-Based Approaches: Young-Do Nam , Youlboong Sung , Ho-Won Chang , Seong Woon Roh , Kyoung-Ho Kim , Sung-Keun Rhee , Jung-Chan Kim , Joo-Yong Kim , Jung-Hoon Yoon , Jin-Woo Bae; J. Microbiol. 2008;46(2):125-136. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0189-1

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Abstract: The undisturbed sediment of Lake Hovsgol (Mongolia) is scientifically important because it represents a record of the environmental changes that took place between the Holocene (the present age) and Pleistocene (the last ice age; 12,000 14C years before present day). Here, we investigated how the current microbial <br>communities change as the depth increases by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA genes of the microbial communities. The microbial diversity, as estimated by the Shannon index, decreased as the depth increased. In particular, significant changes in archaeal diversity were observed in the middle depth (at 39~42 cm depth of total 60 cm depth) that marks the border between the Holocene and Pleistocene. Phylotype belonging to Beta- and Gamma-Proteobacteria were the predominant bacteria and most of these persisted throughout the depth examined. However, as the depth increased, some bacteria <br>(some genera belonging to Beta-Proteobacteria, Nitrospira, and OP8-9) were not detectable while others (some genera belonging to Alpha-, Beta-, Gamma-Proteobacteria) newly deteced by DGGE. Crenarchaea were the predominant archaea and only one phylotype belonging to Euryarchaea was found. Both the <br>archaeal and bacterial profiles revealed by the DGGE band patterns could be grouped into four and three subsets, respectively, subsets that were largely divided by the border between the Holocene and Pleistocene. Thus, the diversity of the current microbial communities in Lake Hovsgol sediments decreases with increasing <br>depth. These changes probably relate to the environmental conditions in the sediments, which were shaped by the paleoclimatic events taking place between the Holocene and Pleistocene.

PCR-DGGE and PCR-RFLP Analyses of the Internal Transcribed Spacer (ITS) of Ribosomal DNA in the Genus Rhizopus: You-Jung Park , Yong-Keel Choi , Byung-Re Min; J. Microbiol. 2003;41(2):157-160.

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Abstract: To estimate genetic relationships within the genus Rhizopus, genetic variations in 20 strains were investigated by DGGE and PCR-RFLP of rDNA ITS region (ITS1, ITS2, 5.8S). The size of the amplified products showed the interspecific polymorphisms, 650 bp, 700 bp, and 900 bp. The DGGE approach allowed the separation of PCR amplicons of the same length according to their sequence variations. When the rDNA ITS region was digested with six restriction enzymes, 20 strains were classified into five RFLP haplotypes. The range of similarity between the 20 strains by PCR-RFLP was 42.3-100%. Based on the results of DGGE and PCR-RFLP, the 20 strains were divided into four groups, R. oryzae, R. stolonifer, R. microsporus and R. homothallicus. Further study of R. homothallicus is required.

Plant Terpene-Induced Expression of Multiple Aromatic Ring Hydroxylation Oxygenase Genes in Rhodococcus sp. Strain T104: Byung-Hyuk Kim , Eun-Taex Oh , Jae-Seong So , Yeonghee Ahn , Sung-Cheol Koh; J. Microbiol. 2003;41(4):349-352.

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Abstract: Recent studies have shown that some of the PCB (polychlorinated biphenyl)-degraders are able to effectively degrade PCB in the presence of monoterpenes, which act as inducers for the degradation pathway. Rhodococcus sp. T104, an effective PCB degrader, has been shown to induce the degradation pathway by utilizing limonenes, cymenes, carvones, and pinenes as sole carbon sources which can be found in the natural environment. Moreover, the strain T104 proved to possess three separate oxidation pathways of limonene, biphenyl, and phenol. Of these three, the limonene can also induce the biphenyl degradation pathway. In this work, we report the presence of three distinct genes for aromatic oxygenase, which are putatively involved in the degradation of aromatic substrates including biphenyl, limonene, and phenol, through PCR amplification and denaturing gradient gel electrophoresis (DGGE). The genes were differentially expressed and well induced by limonene, cymene, and plant extract A compared to biphenyl and/or glucose. This indicates that substrate specificity must be taken into account when biodegradation of the target compounds are facilitated by the plant natural substrates.

The Genetic Diversity Analysis of the Bacterial Community in Groundwater by Denaturing Gradient Gel Electrophoresis (DGGE): Hong-Bum Cho , Jong-Kwang Lee , Yong-Keel Choi; J. Microbiol. 2003;41(4):327-334.

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Abstract: This study employed two PCR-based 16S rDNA approaches, amplified rDNA restriction analysis (ARDRA) and denaturing gradient gel electrophoresis (DGGE), to characterize the bacterial community structure in groundwater. Samples were collected from groundwater for the use by private residences, as well as for industrial and agricultural purposes, in Ansan City. Each PCR product was obtained by PCR with eubacteria 16S rDNA and variable V3 region specific primer sets. After amplification, the 16S rDNA PCR products were digested with 4-base site specific restriction endonucleases, and the restriction pattern analyzed. The genetic diversity and similarity of the groundwater bacterial community was analyzed by eubacteria universal primer sets for the amplification of variable V3 regions of the bacterial 16S rDNA. The result of the bacterial community analysis, by ARDRA and DGGE, revealed the same pattern. The highest diversity was found in groundwater from site G1, which was used in residences. In the DGGE profile, a high intensity band was sequenced, and revealed to be Pseudomonas sp. strain P51.

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